Dataset Readiness Assessment for Training (DRAFT): A Protocol for Auditing High-Dimensional Biological Data

This protocol details Dataset Readiness Assessment for Training (DRAFT), a systematic method for determining if a high-dimensional biological dataset is suitable for developing reliable and equitable machine learning models. Standard model validation often fails to detect when performance is driven by spurious correlations within the dataset, leading to irreproducible findings. DRAFT provides a step-by-step methodology to perform a multiaxis assessment of a dataset's integrity before extensive modeling begins. The assessment comprises three basic protocols to probe the dataset's characteristics: (1) evaluating its potential for generalization by testing baseline model performance and stability under rigorous cross-validation; (2) auditing for inherent biases by analyzing model performance and calibration across demographic subgroups; and (3) measuring its capacity for scientific utility by assessing the stability of predictive features. The Cancer Genome Atlas Lung Adenocarcinoma (TCGA-LUAD) dataset serves as a primary case study to demonstrate DRAFT's ability to reveal a dataset's potential to produce fragile, inequitable, and scientifically uninformative models, even when preliminary modeling achieves high performance metrics. This framework provides a necessary template for vetting datasets, ensuring that subsequent computational models built upon them are robust, equitable, and capable of generating true scientific insight. © 2025 Wiley Periodicals LLC. Support Protocol 1: Environment and software installation via Conda Support Protocol 2: TCGA-LUAD case study: Data acquisition and preparation Basic Protocol 1: Generalization audit: Assessing for overfitting and illusory performance Basic Protocol 2: Equity audit: Assessing for hidden stratification and algorithmic bias Basic Protocol 3: Stability audit: Assessing for spurious discoveries and scientific utility.